Removing cloud cover using Sentinel Toolbox?

ESA's Sen2cor Toolbox removes haze, cirrus and cloud shadows, not dense clouds. It's performed over the same scene, not by mosaicking.

The AC flow is the following from L2A algorithms document:

So, Sen2cor performs an image classification and use this layer to select where to correct pixel values. You can check documentation to know which equation is used in each step.

Thresholds and options are set in GIP file by default (L2A_GIPP.xml), you can change them from this file to overwrite default settings or call them from command line:

<WV_Correction>1</WV_Correction>
<!-- 0: No WV correction, 1: only 940 nm bands, 2: only 1130 nm bands , 3: both regions used during wv retrieval, 4: Thermal region -->
<VIS_Update_Mode>1</VIS_Update_Mode>
<!-- 0: constant, 1: variable visibility -->
<WV_Watermask>1</WV_Watermask>
<!-- 0: not replaced, 1: land-average, 2: line-average -->
<Cirrus_Correction>1</Cirrus_Correction>
<!-- 0: no, 1: yes -->
<BRDF_Correction>0</BRDF_Correction>
<!-- 0: no BRDF correction, 1: , 2: ,11, 12, 22, 21: -->
<BRDF_Lower_Bound>0.22</BRDF_Lower_Bound>
<!-- In most cases, g=0.2 to 0.25 is adequate, in extreme cases of overcorrection g=0.1 should be applied -->

Yes, they are refering to atmospheric correction, to get Bottom of Atmosphere reflectance. The specific tool used for this is called Sen2Cor, which can be installed standalone or part of a package.

• Sen2Cor User Manual

• Cloud detection and correction methodology

What you mentioned about mosaicking images from different dates is another tool for Sentinel-2, called Sen2Three, which is meant to further improve the quality of the AC images generated in L2A.